INSTALL

Shimmer package

Detects changes in next generation sequence reads from tumors by comparing to sequence reads from matched normal samples.

INSTALLATION:

In addition to the software included in this package, the user must have a working copy of 
samtools installed and in ones path (version 0.1.16 or greater), as well as R (version 1.6.1
or greater) with the "statmod" library (available at 
http://cran.r-project.org/web/packages/statmod/index.html).

To install Shimmer system-wide (root permissions required):

    perl Build.PL
    ./Build
    ./Build test
    ./Build install

For local user installation:

    perl Build.PL --install_base $HOME
    ./Build
    ./Build test
    ./Build install

    Then, to access the installed scripts, $HOME/bin must be in your path:

        export PATH=$HOME/bin:$PATH
    
    And $HOME/lib/perl5 must be in your PERL5LIB path:

        export PERL5LIB=$HOME/lib/perl5:$PERL5LIB

    The above export commands can be added to your .profile or .bash_profile
    in order to make them available each time you log in.

USAGE:

Run perldoc shimmer.pl for complete documentation.